MediaWiki currently has the ability to create so called wiki-ref links that can be used as in-line references. This is done by putting single brackets around a naked url. For example http://www.npr.org/news/specials/iraq2003/ can be used as an inline reference in an article by putting [ and ] around the url like so [http://www.npr.org/news/specials/iraq2003/] which renders as [1]. Each such reference is automatically numbered and renumbered each time an article is previewed or saved. However, MediaWiki does not currently have the ability to make automatically-numbered wiki refs for print citations. Here is a proposal explaining one way a full featured reference system may work:

Instead of going directly to the external webpage, an annotation box with the reference information in it is launched for the user.

All citations will be automatically listed in a section at the end of the page titled ==Footnotes==.

Each wiki ref will be represented in the ==Footnotes== section based on its automatically-assigned wiki ref number (one example using JavaScript: see [3] and click on a class number).

The ==Footnotes== section will display the clickable url to the reference.

A pipe character in the wiki ref markup can be used to beautify the resulting footnote list by creating symbolic names. For example, [http://www.npr.org/news/specials/iraq2003/ | NPR Iraq War coverage] will display as *NPR Iraq War coverage in the footnote list (it will appear as a clickable footnote number in the in-line text). Mouse over text will also show the full url and/or the symbolic name.

ISBN numbers and journal reference numbers could be used in place of urls (NOTE: MediaWiki does not currently have the ability to create links based on journal reference numbers).

All other citations may require a pseudo-namespace to function. For example, [footnote:Name of a book, author] (the word 'footnote' would not be displayed in the footnote list). All linking works as above.

All wiki ref links will launch an annotation box that can contain detailed citation information, instead of the current behavior of sending them right to an external webpage. This allows for adding context to the citation.

Printable versions of pages will be usable as is without the need to expand wiki refs into ugly in-line url text (see the printable version of this page to see). URLs instead will be expanded into viewable text only in the ==Footnotes== section.

Encyclopedias and textbooks traditionally do not have in-line text references, however, Wikipedia's credibilty would benefit from easily accessible reference information.

Cons:

It is yet another layer of complexity to our increasingly complex markup.

Encyclopedias and textbooks traditionally do not have in-line text references, so we should not be encouraging such a practice on our projects.

It may require JavaScript and thus some browsers may have to be served pages that have an alternative behavior (such as sending the user to the ==Footnotes== section when he/she clicks on a wiki ref).

It requires a developer to be both motivated to implement this feature and have the time to do so.

Code has been written that will implement footnotes (as of Mediawiki 1.3beta), and been submitted to bugzilla as a patches. This code has not been incorporated into MediaWiki nor are there any plans currently to do so.

The way that it is currently proposed you'd only be allowed to have one reference to each fact. Doing it this way would allow multiple references. If you 'edit' the example you can see the ad hoc tag system.